Current Protein Identity：P61077
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1X23 Crystal structure of ubch5c Deposited 2005-04-19 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
|
Resolution 1.85 Å R-free 0.282 |
| 1X23 Crystal structure of ubch5c Deposited 2005-04-19 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
|
Resolution 1.85 Å R-free 0.282 |
| 1X23 Crystal structure of ubch5c Deposited 2005-04-19 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
|
Resolution 1.85 Å R-free 0.282 |
| 1X23 Crystal structure of ubch5c Deposited 2005-04-19 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain D
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
|
Resolution 1.85 Å R-free 0.282 |
| 2FUH Solution Structure of the UbcH5c/Ub Non-covalent Complex Deposited 2006-01-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
2–147（146 aa）
Fragment：UbcH5c
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 150mM NaCl；Pressure ambient
NMR sample composition
1mM UbcH5c U-15N,13C
25mM sodium phosphate
150mM NaCl | 90% H20
10% D20
NMR sample composition
1mM Ubiquitin U-15N,13C
25mM sodium phosphate
150mM NaCl | 90% H20
10% D20
NMR sample composition
1mM UbcH5c U-15N,13C
1mM Ubiquitin
25mM sodium phosphate
150mM NaCl | 90% H20
10% D20
NMR sample composition
1mM Ubiquitin U-15N,13C
1mM UbcH5c
25mM sodium phosphate
150mM NaCl | 90% H20
10% D20
NMR sample composition
1mM UbcH5c U-15N,13C
1mM Ubiquitin
25mM sodium phosphate
150mM NaCl | 100% D20
NMR sample composition
1mM Ubiquitin U-15N,13C
1mM UbcH5c
25mM sodium phosphate
150mM NaCl | 100% D20
|
Resolution not provided |
| 3L1Z Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme Deposited 2009-12-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；4M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.17 Å R-free 0.279 |
| 3L1Z Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme Deposited 2009-12-14 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；4M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.17 Å R-free 0.279 |
| 3RPG Bmi1/Ring1b-UbcH5c complex structure Deposited 2011-04-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–147（146 aa）
|
Not recorded | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；40% MPD, 0.1 M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.65 Å R-free 0.243 |
| 3RPG Bmi1/Ring1b-UbcH5c complex structure Deposited 2011-04-26 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–147（146 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；40% MPD, 0.1 M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.65 Å R-free 0.243 |
| 3UGB UbcH5c~Ubiquitin Conjugate Deposited 2011-11-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
1–147（147 aa）
Fragment：unp residues 1-147
|
Mutation：C85S | GOL GLYCEROL × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M tri-potassium citrate, 20% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.35 Å R-free 0.252 |
| 4BVU Structure of Shigella effector OspG in complex with host UbcH5c- Ubiquitin conjugate Deposited 2013-06-28 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–147（147 aa）
|
Mutation：YES | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.5；0.1 M TRIS PH 8.5, 20% ETOH
|
Resolution 2.70 Å R-free 0.291 |
| 4R8P Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle Deposited 2014-09-02 | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain L
2–147（146 aa）
Fragment：Residues 2-116 of Ring1B and Residues 2-148 of UbcH5c
Chain N
2–147（146 aa）
Fragment：Residues 2-116 of Ring1B and Residues 2-148 of UbcH5c
|
Not recorded | ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
Modified micro batch under oil；pH 7.5；294 K；25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K
|
Resolution 3.28 Å R-free 0.245 |
| 4S3O PCGF5-RING1B-UbcH5c complex Deposited 2015-03-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
2–147（146 aa）
|
Not recorded | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；277 K；13.5% PEG 550 MME, 10 mM TCEP, 0.1 M MES pH 6.5, 100 mM KCl, VAPOR DIFFUSION, temperature 277K
|
Resolution 2.00 Å R-free 0.237 |
| 4S3O PCGF5-RING1B-UbcH5c complex Deposited 2015-03-23 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–147（146 aa）
|
Not recorded | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；277 K；13.5% PEG 550 MME, 10 mM TCEP, 0.1 M MES pH 6.5, 100 mM KCl, VAPOR DIFFUSION, temperature 277K
|
Resolution 2.00 Å R-free 0.237 |
| 5EGG Crystal structure of human ubiquitin-conjugating enzyme UBCH5C Deposited 2015-10-27 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；2% v/v Tacsimate pH 4.0, 0.1 M Sodium acetate trihydrate pH 4.6, 16% w/v Polyethylene glycol 3350
|
Resolution 1.76 Å R-free 0.253 |
| 5IFR Structure of the stable UBE2D3-UbDha conjugate Deposited 2016-02-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
2–147（146 aa）
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；200mM tripotassium citrate, 20% PEG 3350
|
Resolution 2.20 Å R-free 0.243 |
| 6CP0 SdcA in complex with the E2, UbcH5C Deposited 2018-03-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–147（147 aa）
|
Mutation：C85S | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.5 M ammonium sulfate, 3% glycerol, 0.1 M HEPES pH 7.5
|
Resolution 3.01 Å R-free 0.261 |
| 6T7F RCR E3 ligase E2-Ubiquitin transthiolation intermediate Deposited 2019-10-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
2–147（146 aa）
|
Mutation：C21S, S22R, C107S, C111S | ZN ZINC ION × 6 LWZ 3,3-bis(sulfanyl)-~{N}-(1~{H}-1,2,3-triazol-4-ylmethyl)propanamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；0.85 M sodium citrate, 100 mM sodium chloride, 100 mM Tris-HCl pH 8.0
|
Resolution 2.58 Å R-free 0.256 |
| 7JZV Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Deposited 2020-09-02 | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain A
2–147（146 aa）
|
Mutation：UbcH5c C85K | ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain P
2–147（146 aa）
|
Not recorded | ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.28 Å |
| 8AMS Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin Deposited 2022-08-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain A
1–147（147 aa）
Chain B
1–147（147 aa）
|
Not recorded | GOL GLYCEROL × 9 ZN ZINC ION × 4 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.2 M sodium formate, 0.1 M bis-tris propane, 20% PEG 3350
|
Resolution 2.40 Å R-free 0.233 |
| 8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain L
1–147（147 aa）
|
Mutation：C21I, C107A, C111D, L119K | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain L
2–147（146 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain L
2–147（146 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–147（146 aa）
|
Not recorded | CL CHLORIDE ION × 7 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
|
Resolution 2.34 Å R-free 0.236 |
| 8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain a
2–147（146 aa）
|
Not recorded | CL CHLORIDE ION × 14 GOL GLYCEROL × 2 ZN ZINC ION × 2 NA SODIUM ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
|
Resolution 2.34 Å R-free 0.236 |
| 8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–147（146 aa）
|
Not recorded | CL CHLORIDE ION × 17 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
|
Resolution 2.30 Å R-free 0.206 |
| 8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain a
2–147（146 aa）
|
Not recorded | CL CHLORIDE ION × 19 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
|
Resolution 2.30 Å R-free 0.206 |
| 8UQA Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker Deposited 2023-10-23 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain K
2–147（146 aa）
|
Mutation：C85K in UbcH5c | NA SODIUM ION × 3 ZN ZINC ION × 2 CL CHLORIDE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.0 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
|
Resolution 2.05 Å R-free 0.231 |
| 8UQB Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1) Deposited 2023-10-23 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–147（146 aa）
|
Mutation：C85K in UbcH5c | ZN ZINC ION × 2 CL CHLORIDE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 50 mM BIS-TRIS propane, pH 7.0, 1 M NaCl
|
Resolution 2.48 Å R-free 0.260 |
| 8UQC Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 2) Deposited 2023-10-23 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–147（146 aa）
|
Mutation：C85K in UbcH5c | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
|
Resolution 2.61 Å R-free 0.252 |
| 8UQD Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (condition 2. RING not modeled in density) Deposited 2023-10-23 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
2–147（146 aa）
|
Mutation：C85K in UbcH5c | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
|
Resolution 3.89 Å R-free 0.322 |
| 8UQE Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 26-residue linker (RING not modeled in density) Deposited 2023-10-23 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
2–147（146 aa）
|
Mutation：S22R,C85K in UbcH5c | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (10 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M imidazole, pH 6.5, 1.0 M sodium acetate
|
Resolution 3.56 Å R-free 0.268 |
| 8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain K
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain K
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.39 Å |
| 8X7K Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Deposited 2023-11-24 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain K
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain K
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 9LPK Structure of human PADI6-UHRF1-UBE2D3 complex Deposited 2025-01-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain D
1–147（147 aa）
Chain E
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.03 Å |
| 9V9Q Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain P
1–147（147 aa）
|
Mutation：C85S, S22R | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 2.80 Å |
| 9V9R Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain P
1–147（147 aa）
|
Mutation：C85S, S22R | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.20 Å |